galaaz 0.4.2 → 0.4.5

data/lib/R/eng_ruby.R~

@@ -1,63 +0,0 @@
-# define the ruby engine for processing Ruby chunks in
-# rmarkdown
-eng_ruby = function(options) {
-  block_code = paste(options$code, collapse = "\\n");
-  code = paste0("GalaazUtil.exec_ruby(", 
-                   shQuote(block_code), 
-                  ")
-                ");
-
-  # png(paste0("gknit_files/figure-html/", options$label, ".png"));
-
-  keep = options$fig.keep
-  keep.idx = NULL
-  if (is.numeric(keep)) {
-    keep.idx = keep
-    keep = "index"
-  }
-
-  tmp.fig = tempfile(); on.exit(unlink(tmp.fig), add = TRUE)
-
-  # open a device to record plots
-  if (chunk_device(options$fig.width[1L], options$fig.height[1L], keep != "none",
-                   options$dev, options$dev.args, options$dpi, options, tmp.fig)) {
-    # preserve par() settings from the last code chunk
-    if (keep.pars <- opts_knit$get("global.par"))
-      par2(opts_knit$get("global.pars"))
-    showtext(options$fig.showtext)  # showtext support
-    dv = dev.cur()
-    on.exit({
-      if (keep.pars) opts_knit$set(global.pars = par(no.readonly = TRUE))
-      dev.off(dv)
-    }, add = TRUE)
-   }
-
-  # guess plot file type if it is NULL
-  if (keep != "none" && is.null(options$fig.ext))
-    options$fig.ext = dev2ext(options$dev)
-
-  # out = eval.polyglot("ruby", code);
-  res = eval.polyglot("ruby", code);
-
-# rearrange locations of figures
-  figs = find_recordedplot(res)
-  if (length(figs) && any(figs)) {
-    if (keep == 'none') {
-      res = res[!figs] # remove all
-    } else {
-      if (options$fig.show == 'hold') res = c(res[!figs], res[figs]) # move to the end
-      figs = find_recordedplot(res)
-      if (length(figs) && sum(figs) > 1) {
-        if (keep %in% c('first', 'last')) {
-          res = res[-(if (keep == 'last') head else tail)(which(figs), -1L)]
-        } else {
-          # keep only selected
-          if (keep == 'index') res = res[which(figs)[keep.idx]]
-          # merge low-level plotting changes
-          if (keep == 'high') res = merge_low_plot(res, figs)
-        }
-      }
-    }
-}
-  engine_output(options, block_code, res)
-}

data/lib/R_interface/capture_plot.rb~

@@ -1,23 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-

data/lib/R_interface/r.rb~

@@ -1,121 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-
-require_relative 'robject'
-require_relative 'rsupport'
-
-module R
-
-  RCONSTANTS = ["LETTERS", "letters", "month.abb", "month.name", "pi"]
-
-  #----------------------------------------------------------------------------------------
-  #
-  #----------------------------------------------------------------------------------------
-
-  def self.method_missing(symbol, *args, &block)
-    
-    if (block_given?)
-      val = R::Support.process_missing(symbol, false, *args)
-      return R::Support.new_scope(symbol, val, *args, &block)
-    end
-
-    R::Support.process_missing(symbol, false, *args)
-
-  end
-
-  #----------------------------------------------------------------------------------------
-  #
-  #----------------------------------------------------------------------------------------
-
-  def self.internal_eval(symbol, *args)
-    R::Support.process_missing(symbol, true, *args)
-  end
-
-  #----------------------------------------------------------------------------------------
-  # Checks to see if the given libs are installed in R and if not, install them
-  # @param libs [Array] Array of strings with the names of the libraries to check and
-  # install
-  #----------------------------------------------------------------------------------------
-
-  def self.install_rlibs(*libs)
-
-    packages = R.c(libs)
-
-    new_packages = packages[!(packages._ :in, R.installed__packages[:all, "Package"])]
-    if(new_packages.size > 0)
-      puts "The following packages are missing and will be installed:\n #{new_packages}"
-      R.install__packages(new_packages)
-    end
-    
-  end
-
-  #----------------------------------------------------------------------------------------
-  #
-  #----------------------------------------------------------------------------------------
-
-  def self.install_and_loads(*libs)
-    R.install_rlibs(*libs)
-    libs.each { |lib| R.require lib }
-  end
-  
-end
-
-# define methods for accessing indexed object: Vector, Lists
-require_relative 'rindexed_object'
-# define methods for accessing multi dimensional indexed objects: Matrix, DataFrames
-require_relative 'rmd_indexed_object'
-# Binary operators: '+', '-', etc
-require_relative 'rbinary_operators'
-# Unary operators: '!', '@-', etc
-require_relative 'runary_operators'
-# Definition of R Vector
-require_relative 'rvector'
-# Definition of R Lists
-require_relative 'rlist'
-# Definition of R Matrix
-require_relative 'rmatrix'
-# Definition of R DataFrame
-require_relative 'rdata_frame'
-# Definition of R Closure (functions)
-require_relative 'rclosure'
-# Definition of R Expression
-require_relative 'rexpression'
-# Definition of R Environment
-require_relative 'renvironment'
-# Definition of R Language
-require_relative 'rlanguage'
-# Definition of R Symbol
-require_relative 'rsymbol'
-# Access to package symbols
-require_relative 'rpkg'
-
-# Defines the E module for creating R expressions
-require_relative 'expression'
-# Ruby class extensions.  Extends Symbol to allow the creation of
-# expressions using Symbol: (:x > 10)
-require_relative 'ruby_extensions'
-# Class to allow R calling back into Ruby
-require_relative 'ruby_callback'
-
-# Util to execute Ruby code in a string redirecting stdout
-require_relative 'util/exec_ruby'

data/lib/R_interface/rdevices.rb~

@@ -1,27 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-
-dir = File.dirname(File.expand_path('.', __FILE__))
-src = "#{dir}/capture_plot.R"
-
-R.source(src)

data/lib/gknit.rb~

@@ -1,26 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-
-require 'galaaz'
-
-puts "gknit loaded"

data/lib/gknit/knitr_engine.rb~

@@ -1,102 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-
-R.install_and_loads('knitr', 'rmarkdown')
-
-# dir = File.dirname(File.expand_path('.', __FILE__))
-# src = "#{dir}/R/eng_ruby.R"
-
-class KnitrEngine
-
-  attr_reader :keep
-
-  #--------------------------------------------------------------------------------------
-  # opens a device for plot recording.  Method chunk_device in knitr is not exported,
-  # so it cannot yet be accessed by Galaaz.  Need to develop a local function that calls
-  # the non-exported function.
-  #--------------------------------------------------------------------------------------
-
-  R::Support.eval(<<-R)
-    _ck_dv = function(width, height, record = TRUE, dev, dev.args, dpi, options, 
-                      tmp = tempfile()) {
-        knitr:::chunk_device(width, height, record, dev, dev.args, dpi, options, tmp)
-      }
-    R
-
-  #--------------------------------------------------------------------------------------
-  # The showtext package, is able to support more font formats and more graphics
-  # devices, and avoids using external software such as Ghostscript. showtext makes it
-  # even easier to use various types of fonts (TrueType, OpenType, Type 1, web fonts,
-  # etc.) in R graphs.
-  #--------------------------------------------------------------------------------------
-
-  R::Support.eval(<<-R)
-    showtext = function() {
-      print("showtext beginning")
-      showtext::showtext_begin()
-    }
-  R
-    
-  #--------------------------------------------------------------------------------------
-  # Process the fig.keep chunk option
-  # @bug this does not what it should
-  #--------------------------------------------------------------------------------------
-
-  def self.fig_keep(keep)
-    puts "checking fig_keep options"
-    
-    @keep = keep
-    puts @keep
-    
-    @keep.idx = nil
-    
-    if (@keep.is__numeric << 0)
-      puts "keep is numeric"
-      
-      @keep.idx = keep
-      @keep = "index"
-    end
-
-    puts @keep
-    
-  end
-
-  #--------------------------------------------------------------------------------------
-  # Process the chunk options
-  #--------------------------------------------------------------------------------------
-  
-  def self.process_options(options)
-    fig_keep(options.fig__keep)
-  end
-
-  #--------------------------------------------------------------------------------------
-  # Adds the new knitr engine to the list of engines
-  # @param spec [Hash] hash with only one pair containing the machine key and the engine
-  #    function
-  #--------------------------------------------------------------------------------------
-  
-  def add(spec)
-    (~:knit_engines).set.call(spec)
-  end
-  
-end

data/lib/gknit/ruby_engine.rb~

@@ -1,72 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-
-# Ruby engine for processing Ruby chunks
-eng_ruby = Proc.new do |options|
-
-  begin
-    # read the chunk code
-    code = R.paste(options.code, collapse: "\n") << 0
-    
-    # process the chunk options
-    KnitrEngine.process_options(options)
-    
-    # opens a device for the current chunk for plot recording. Knitr provides
-    # method chunck_device for that, but it is a non-exported method.  Galaaz
-    # does not yet provide a way to accessing non-exported methods, so, the ck_dv
-    # local method was developed that just calls chunk_device.
-    if (R._ck_dv(options.fig__width[1], options.fig__height[1], options.dev,
-                 options.dev__args, options.dpi, options, record: true) << 0)
-
-      puts "===================================="
-      puts "fig.showtext is element?"
-      puts R.is__element('fig.showtext', options)
-      puts options['fig.showtext']
-      puts "===================================="
-      
-      if (R.is__element('fig.showtext', options) << 0)
-        puts "==============================="
-        puts options.fig__showtext
-        puts options.fig__showtext << 0
-      end
-      
-      R.showtext if (R.is__element('fig.showtext', options) << 0) &&
-                    (options.fig__showtext << 0) == true
-      dv = R.dev__cur
-    end
-    
-    # executes the code
-    res = GalaazUtil.exec_ruby(code)
-    
-    # formats and outputs the code and results
-    R.engine_output(options, options.code, res)
-
-  ensure
-    R.dev__off(dv)
-  end
-  
-end
-
-ruby_engine = KnitrEngine.new
-ruby_engine.add(ruby: eng_ruby)
-

data/lib/util/inline_file.rb~

@@ -1,23 +0,0 @@
-# -*- coding: utf-8 -*-
-
-##########################################################################################
-# @author Rodrigo Botafogo
-#
-# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
-# and distribute this software and its documentation, without fee and without a signed 
-# licensing agreement, is hereby granted, provided that the above copyright notice, this 
-# paragraph and the following two paragraphs appear in all copies, modifications, and 
-# distributions.
-#
-# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
-# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
-# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
-# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
-# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
-# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
-# OR MODIFICATIONS.
-##########################################################################################
-